Lichen community dataset from coastal fog oases and Andean shrublands of southern Peru
Description
Lichen community dataset from coastal fog oases (lomas) and Andean shrublands of southern Peru. Contains the species-by-station abundance matrix at the sampling-unit level, the taxonomic checklist with growth form and substrate annotations, station-level environmental metadata, processed community matrices used in beta diversity analyses, and R scripts for data preparation, alpha diversity, beta diversity partitioning (Baselga framework), functional analyses, and indicator species analysis. Includes 53 lichen species across 8 sectors, 40 sampling stations, and 200 sampling units in the Moquegua region, southern Peru.
Files
Steps to reproduce
Field data were collected in southern Peru across eight sectors representing two ecosystem types: coastal fog oases (Tacahuay, Huacaluna, and Amoquinto) and Andean shrublands (Altarani, Alto Coscore, Calientes, Charaque, and Tala). The sampling design comprised 40 stations and 200 sampling units (five sampling units per station). Lichen abundance was recorded using a standardized Braun-Blanquet cover-abundance approach, and species were identified using morphological and chemical characters. To reproduce the analytical workflow, download all repository files into a single working directory and open R or RStudio (R v. 4.5.1 or later). The main input files are species_abundance_matrix.csv and taxonomic_checklist.csv. Run the scripts in the following order: 00_style_guide_jvs.R, 01_Setup_Data_JVS.R, 02_Alpha_Inventory_JVS.R, 03_Beta_Diversity_JVS.R, 04_Functional_Environmental_JVS.R, 05_Diagnostic_Species_JVS.R, and 06_Figures_Publication_JVS.R. The setup script performs data cleaning, quality control, incorporation of the Amoquinto zero-detection sector, and generation of processed community matrices and station-level metadata. Subsequent scripts reproduce the taxonomic inventory, sample completeness analyses, alpha diversity, beta diversity partitioning, PERMANOVA, PERMDISP, PCoA, LCBD, functional composition analyses, ecosystem- and sector-level diagnostic species analyses (IndVal.g), and final publication-ready figures. Output files are written automatically to the resultados directory. Amoquinto was sampled using the same standardized protocol as all other sectors, but no lichen species were recorded under this design. For this reason, Amoquinto was retained in richness and detection summaries but excluded from species-composition analyses that require non-empty community matrices.